tbuckley/cabot-search huggingface dataset:
Abstract 2428: Cancer stem cells maintain stemness via autocrine activation of the IFN/JAK/STAT signaling pathway
Authors: Aidan Li, Xuetao Bai, Na Li, Shurui Cai, Ananya Banerjee, Kousalya Lavudi, Linzhou Wang, Qianyun Ge, Yajing Yang, Qi-En Wang
Journal: Cancer Research (2023)

Abstract Interferons (IFNs) and Janus Kinase/Signal Transducer and Activator of Transcription (JAK/STAT) signaling are best known for their roles in immunity. However, recent work has suggested that both IFNs and the JAK/STAT pathways are associated with tumor growth and progression, as well as the maintenance of cancer stem cell (CSC) populations. To better understand the regulation of the CSC population maintenance by the IFN/JAK/STAT signaling pathway, we enriched CSCs from a panel of non-small cell lung cancer (NSCLC) cell lines by using spheroid culture and determined the phosphorylation of STAT1. We found that sphere cells exhibit increased level of pSTAT1-Y701 compared to their corresponding bulk cells. We further determined the expression level of a few interferon-stimulated genes (ISGs) and found that sphere cells possess enhanced expression of ISG54 and ISG56 genes, which are normally induced by type I IFN (IFN-I), as well as IFNA and IFNB. These results indicate that the IFN-I/STAT1 signaling is highly activated in CSCs, which produce and secrete increased amount of IFN-I. To directly show the effect of IFN-I on the stemness of NSCLC cells, we treated NSCLC cells with IFNβ, and found that IFNβ can significantly enhance the expression of SOX2, a stem cell-specific transcription factor; Inhibition of the JAK signaling blocked both basal and IFNβ-induced SOX2 expression. In addition, knockdown of STAT1 also reduced SOX2 expression, indicating that STAT1 activation plays an important role in mediating IFN-induced enhancement of stemness. Finally, the ChIP assay demonstrated that STAT1 protein can bind to the promoter region of the SOX2 gene to serve as a transcription factor. In summary, our results indicate that CSCs produce and secrete IFN-I via their enhanced JAK/STAT1 signaling. The secreted IFN-I can bind to the receptor on the CSCs, further activate their JAK/STAT1 signaling, promoting the expression of SOX2 and maintenance of stemness of CSCs via an autocrine manner. Citation Format: Aidan Li, Xuetao Bai, Na Li, Shurui Cai, Ananya Banerjee, Kousalya Lavudi, Linzhou Wang, Qianyun Ge, Yajing Yang, Qi-En Wang. Cancer stem cells maintain stemness via autocrine activation of the IFN/JAK/STAT signaling pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2428.
Abstract 936: Clinicogenomic predictors for the pattern of failure in high-grade glioma
Authors: Joo Ho Lee, Byung-Hee Kang, Seungbok Lee
Journal: Cancer Research (2023)

Abstract Background: High-grade gliomas, the most common primary brain tumors, are highly lethal, and treatment options remain limited. Despite advances in genomic technologies, there are few molecular biomarkers to guide precision medicine for high-grade glioma. Here, we aimed to identify the clinicogenomic features associated with its prognosis and recurrence patterns. Materials/Methods: Our single-institution retrospective analysis included 223 patients diagnosed with high-grade gliomas who underwent next-generation sequencing targeting 82 brain tumor-relevant genes. We categorized them according to the 2021 WHO classification, and their clinicopathological statuses, treatment characteristics, survival, and genomic profiles were analyzed. Results: The most common genomic variants were TERT promoter (51%), TP53 (39%), IDH1/2 (18%), NF1 (13%), ATRX (12%), PTEN (11%), PIK3CA (9%), SETD2 (7%), and H3F3A (6%) mutation. Regarding copy number variants, amplification of EGFR (21%), PDGFRA (11%), CDK4 (9%) and loss of CDKN2A/2B (55%), PTEN (29%), 19q (17%), NF2 (14%), and RB1 (10%) were the most common copy number aberrations. At a median follow-up of 18 months (range, 2-54 months), 174 patients (78%) had progression or recurrences. A total of 15.2% of our patients were re-classified under the 2021 WHO classification, and there was a clear separation of overall survival(OS) and progression-free survival(PFS) curves between grade 3 and 4 groups using the revised grading system. On multivariate cox regression analysis, MYCN amplification (HR 6.08, p = 0.002) and SETD2 mutation (HR 0.19, p =0.06) were independent predictors of OS and PFS. Conclusion: The assessment of genomic characteristics in conjunction with the pattern of failure for high-grade glioma aids in identifying patients who are likely to benefit from personalized medicine. The 2021 WHO grading system explains survival differences between grade 3 and 4 tumors better than the 2016 WHO classification dose. We identified SETD2 mutation and MYCN as prognostic biomarkers with potential therapeutic implications in patients with high-grade glioma. Citation Format: Joo Ho Lee, Byung-Hee Kang, Seungbok Lee. Clinicogenomic predictors for the pattern of failure in high-grade glioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 936.
Abstract 5961: Inhibition of AURKA destabilizes glioblastoma primary cilia and sensitizes cells to tumor treating fields (TTFields) in vitro and ex vivo
Authors: Jia Tian, Julianne Mallinger, Ping Shi, Dahao Ling, Loic Deleyrolle, Min Lin, Habibeh Khoshbouei, Matthew Sarkisian
Journal: Cancer Research (2023)

Abstract Tumor Treating Fields (TTFields) can prolong survival of patients with glioblastoma (GBM), but GBM cells still escape this therapy requiring an urgent need for new or adjunct treatments. Recently we reported that TTFields disrupt primary cilia on GBM cells which lowers resistance to standard of care temozolomide chemotherapy. Here we asked if concomitant or sequential treatment of TTFields with other agents that interfere with GBM ciliogenesis enhance TTFields efficacy. Aurora Kinase A (AURKA) plays both a role in promoting cilia disassembly and regulating GBM growth in xenograft models. We found that within 24hr of treatment with the AURKA inhibitor, Alisertib, there was surprising and significant decrease in GBM cilia frequency across multiple GBM patient derived lines. However, similar Alisertib treatment did not affect neuronal or glial cilia frequencies in mixed primary cell cultures from mouse forebrain. Notably, overnight treatment of patient GBM biopsy ex vivo with Alisertib also resulted in reduced cilia frequency within the tumor tissue. Next, we co- or sequentially treated several different GBM patient cell lines with 24hr of 200kHz TTFields together with or followed by 250nM or 1µM Alisertib and examined the subsequent expansion of cells in vitro. We observed a significant synergistic reduction in cell proliferation compared to either treatment alone. However, this synergistic effect does not appear to be cilia-dependent as dual treatment reduction in proliferation was still observed in cell lines lacking different key cilia genes or in GBM cells that naturally lack cilia. Considering Alisertib crosses the blood brain barrier and inhibits intracranial growth of tumors, our data warrant investigation of whether concomitant or sequential treatment of TTFields and Alisertib in vivo can further prolong survival. Citation Format: Jia Tian, Julianne Mallinger, Ping Shi, Dahao Ling, Loic Deleyrolle, Min Lin, Habibeh Khoshbouei, Matthew Sarkisian. Inhibition of AURKA destabilizes glioblastoma primary cilia and sensitizes cells to tumor treating fields (TTFields) in vitro and ex vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5961.
Abstract 4668: <i>In-vitro</i> modeling of tumor-associated macrophages in glioblastoma
Authors: Hasan Alrefai, Andee M. Beierle, Taylor L. Schanel, Lauren C. Nassour, Joshua C. Anderson, Patricia H. Hicks, Christopher D. Willey
Journal: Cancer Research (2023)

Abstract BACKGROUND: The Glioblastoma (GBM) tumor microenvironment (TME) is comprised of a plethora of cancerous and non-cancerous cells that contribute to GBM growth, invasion, and chemo- and radio-resistance. In-vitro models of GBM typically fail to incorporate multiple cell types. Some groups have addressed this problem by employing 3D bioprinting to incorporate macrophages, astrocytes, and other parenchymal cells in an extracellular matrix. However, these models also use serum-containing media, which has been shown to cause GBM brain-tumor initiating cells to lose their stem-like properties, and IL-4/13 polarized macrophages (M2), even though tumor-associated macrophages (TAMs) do not adhere to the traditional M2 phenotype. Taken together, these observations highlight a critical need to develop physiologically accurate in-vitro model systems for GBM. METHODS: THP-1 monocytes were transitioned from serum-containing RPMI 1640 to serum-free CTS™ AIM V™ SFM and TheraPEAKTM X-VIVOTM-15 Serum-free Hematopoietic Cell Medium. Monocytes were stimulated towards a macrophage-like state with PMA and polarized by co-culturing them with GBM patient-derived xenograft (PDX) lines, using transwell inserts. dPCR, a cytokine array, and a phagocytosis assay were used to characterize macrophages polarized by this method relative to classically polarized resting (M0), pro-inflammatory (M1), and anti-inflammatory (M2) macrophages. RESULTS: There was no significant difference in proliferation rates up to 48 hours for THP-1 monocytes grown in serum-free CTS AIM V or X-VIVO-15 media compared to serum-containing RPMI 1640. At 72 hours, both serum-free alternatives had slightly decreased proliferation relative to the serum-containing RPMI 1640; however, the X-VIVO-15 had higher proliferation relative to the CTS AIM V (p&amp;lt;0.0001). THP-1 macrophages polarized towards a tumor-supportive phenotype by the GBM PDX cell line, JX39P-RT, did not recapitulate the cytokine expression profile of any other polarization group. M2 macrophages had significantly higher phagocytic capacity (25%) of JX39P-RT relative to M0, M1, and TAMs (&amp;lt;15%, p&amp;lt;0.01). CONCLUSIONS: We have demonstrated a serum-free method by which we can polarize macrophages towards a GBM-supportive phenotype. This high-fidelity method of modeling TAMs in GBM will aid in the development of innate immunomodulatory therapeutics that may one day enter the clinic in hopes of improving GBM outcomes. Citation Format: Hasan Alrefai, Andee M. Beierle, Taylor L. Schanel, Lauren C. Nassour, Joshua C. Anderson, Patricia H. Hicks, Christopher D. Willey. In-vitro modeling of tumor-associated macrophages in glioblastoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4668.
Abstract 1723: Ferroptosis is a novel therapeutic target for RB1 deficient lethal prostate cancer
Authors: Mu-En Wang, Jiaqi Chen, Yi Lu, Jinjin Wy, Jianhong Ou, John Asara, Andrew Armstrong, Qianben Wang, Lei Li, Yuzhuo Wang, Jiaoti Huang, Ming Chen
Journal: Cancer Research (2023)

Abstract Background: Although the development of next-generation antiandrogens has significantly extended the survival time of patients with metastatic castration-resistant prostate cancer (mCRPC), drug resistance inevitably developed over time. Therefore, the identification of novel therapeutic strategies targeting mCRPC is urgent. RB1 deficiency is a common genetic event and contributes to the development of therapy resistance and poor prognosis in prostate cancer. However, effective therapies against RB1-deficient lethal prostate cancer remain elusive. Here we determined how RB1 regulates the sensitivity of prostate cancer cells to ferroptosis, a form of regulated cell death driven by iron-dependent lipid peroxidation, and whether we can exploit ferroptosis for the treatment of RB1 deficient lethal prostate cancer. Methods: To determine how RB1 regulates ferroptosis in prostate cancer, we generated RB1 stable knockdown prostate cancer cell lines using lentivirus-delivered shRNAs. We compared cellular sensitivity to ferroptosis and associated lipid peroxidation between control and RB1 stable knockdown prostate cancer cells. Using western blotting, qPCR, and ChIP analyses, we examined the regulation of ferroptosis by RB1. We also evaluated the therapeutic efficacy of ferroptosis inducers in cell-derived xenograft, patient-derived xenograft, and genetically engineered mouse models. Results: Our studies revealed that RB1 deficiency sensitizes prostate cancer cells to ferroptosis. Mechanistically, we found that the E2F family of transcription factors directly binds and activates the ACSL4 promoter and that RB1 inhibits ferroptosis by suppressing E2F-mediated ACSL4 transcriptional activation. More importantly, our preclinical studies demonstrated that induction of ferroptosis by JKE-1674, a recently discovered ferroptosis inducer, significantly blocks RB1 deficient prostate tumor growth and metastasis, and improves the overall survival of mice in the absence of obvious toxicity. Conclusions: Our findings uncover an RB1/E2F/ACSL4 molecular axis that governs ferroptosis and also suggest a new approach to the treatment of RB1-deficient lethal prostate cancer. Citation Format: Mu-En Wang, Jiaqi Chen, Yi Lu, Jinjin Wy, Jianhong Ou, John Asara, Andrew Armstrong, Qianben Wang, Lei Li, Yuzhuo Wang, Jiaoti Huang, Ming Chen. Ferroptosis is a novel therapeutic target for RB1 deficient lethal prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1723.
Abstract 448: Computational discovery and experimental validation of splicing-derived neoantigens
Authors: Hasan Ekrem Zumrut, Kendall Anderson, Miguel Manzanares, Shaleigh Smith, Sakshi Gera, Nayab Habib, Sanjana Shah, Devon Trahan, Martin Akerman, Gayatri Arun
Journal: Cancer Research (2023)

Abstract RNA splicing is a central step in the regulation of gene expression, leading to the accurate assembly of viable mRNA isoforms. Errors in the splicing process are common in cancer and lead to the production of tumor-specific mRNAs that often encode for neoantigen peptides. Such neoantigens cannot be discovered using conventional DNA-based tools; they require specialized software for alternative splicing analysis using RNA-seq data. Envisagenics has developed SpliceIOTM, a proprietary software platform for splicing-derived neoantigen discovery. SpliceIO uses RNA-seq data to uncover extracellular neoantigens encoded by transmembrane proteins or presented to immune cells through the MHC complex. Using SpliceIO, we have analyzed roughly 8,000 RNA-seq samples from 4 different cancers and 14 normal tissue types. Each dataset first undergoes an unsupervised clustering analysis using SpliceSliceTM to stratify patients into subpopulations based on similar aberrations in splicing machinery. We then leverage SpliceIO to identify splicing-derived, tumor-specific neoantigens enriched in these cohorts. SpliceIO incorporates features, such as protein localization, MHC binding affinity, epitope accessibility and cancer relevance of the gene to help select tumor specific targets with the highest therapeutic potential. Here, we summarize the discovery and validation of novel splicing-derived neoantigens identified using SpliceIO. To validate neoantigen candidates, we performed isoform expression quantification at the RNA and protein levels using PCR, RNA-FISH, western blot and mass spectrometry. Our experiments confirmed several neoantigen candidates encoded by tumor-specific RNA isoforms, that are translated and localized to the cellular membrane. Interestingly, one of the candidates is an endoplasmic reticulum protein that exhibits cassette exon skipping in approximately 24% of TNBC tumors. Fluorescence microscopy experiments demonstrate that the TNBC-specific isoform of the protein is localized to plasma membrane but not the ER, suggesting that alternative splicing can alter protein localization. Together, our results demonstrate the potential of RNA splicing analysis for the discovery of novel immunotherapeutic targets. Citation Format: Hasan Ekrem Zumrut, Kendall Anderson, Miguel Manzanares, Shaleigh Smith, Sakshi Gera, Nayab Habib, Sanjana Shah, Devon Trahan, Martin Akerman, Gayatri Arun. Computational discovery and experimental validation of splicing-derived neoantigens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 448.
Abstract 975: Treatment prognostic signature of patients with non-small cell lung cancer: a retrospective single-institutional study
Authors: Margaret R. Smith, Yuezhu Wang, Ralph D' Agostino, Yin Liu, Jimmy Ruiz, Thomas Lycan, George Oliver, Umit Topaloglu, Jireh Pinkney, Mohammed N. Abdulhaleem, Michael D. Chan, Michael Farris, Jing Su, Fei Xing
Journal: Cancer Research (2023)

Abstract Introduction: Currently, several types of treatment can be used to treat non-small cell lung cancer (NSCLC) depending on a potential druggable mutation or stage of cancer. However, a limited number of biomarkers are available to guide clinicians in selecting the most effective therapy for all patients. Methods: The clinical characteristics of 642 NSCLC patients and tumor sequencing data were collected retrospectively at Atrium Health Wake Forest Baptist. Cox-proportional hazard regression models were fit to identify mutations that were “beneficial” (hazard ratio &amp;lt; 1) or “detrimental” (hazard ratio &amp;gt; 1) for patients on different treatment regimens, followed by the generation of mutation composite scores (MCS) for each treatment. The overall survival (OS) of patients receiving each treatment was plotted based on the patients’ MCS, and receiver operating characteristics (ROC) curves tested the predictive power of each MCS for each treatment group. We also identified novel co-occurring and mutually exclusive mutations in each treatment group by mutation interaction analysis. Results: We identified treatment-specific mutations associated with either a better or worse OS. The MCS generated for each treatment group significantly enhanced the prediction power compared to a single mutation with limited application in patients with rare mutations. Mutation signatures to chemotherapy (NTRK1, FBXW7, BRAF, MPL, KRAS, and GATA3) and immunotherapy (MAP2K1, EGFR, CDK4, NTRK1, and NOTCH1) have a comparable prediction power with actual clinical response. Conclusions: NSCLC patients’ responses to specific treatments are diverse because of tumor heterogeneity. Our work demonstrates how analyzing patients’ sequencing data facilitates the clinical selection of optimized treatment strategies. Citation Format: Margaret R. Smith, Yuezhu Wang, Ralph D' Agostino, Yin Liu, Jimmy Ruiz, Thomas Lycan, George Oliver, Umit Topaloglu, Jireh Pinkney, Mohammed N. Abdulhaleem, Michael D. Chan, Michael Farris, Jing Su, Fei Xing. Treatment prognostic signature of patients with non-small cell lung cancer: a retrospective single-institutional study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 975.
Abstract 1759: Targeting adaptation to cancer treatment by drug combinations
Authors: Augustin Luna, Heping Wang, Gonghong Yan, Xubin Li, Ozgun Babur, Gordon Mills B. Mills, Chris Sander, Anil Korkut
Journal: Cancer Research (2023)

Abstract Adaptation of tumors to therapeutic interventions contributes to dismal long-term patient outcomes. Adaptation to therapy involves co-action of functionally related proteins that together activate cell survival programs and compensate for the therapeutic impact. Oncogenic dependencies to such adaptive events, however, can generate new therapeutic vulnerabilities that can be targeted with drug combinations. The precision medicine approaches in which targeted drugs are matched to pre-existing genomic aberrations fail to address the adaptive responses and resulting vulnerabilities. Here, we provide the mathematical formulation, implementation and validation of the TargetScore method. The TargetScore identifies collective adaptive responses to targeted interventions as concurrent changes of phospho-proteins that are connected within a signaling network. Based on the adaptive responses, the method predicts drug-induced vulnerabilities. Using TargetScore, we inferred the adaptive responses with short-term (i.e., days) stress and long-term (i.e., months) acquired resistance to inhibitors of anti-apoptotic mediators, MCL1 and BCL2. With experiments guided by the predictions, we identified synergistic interactions between inhibitors of PARP, SHP2, and MCL1 in breast cancer cells. TargetScore is readily applicable to existing precision oncology efforts by matching targeted drug combinations to emerging molecular signatures under therapeutic stress. Citation Format: Augustin Luna, Heping Wang, Gonghong Yan, Xubin Li, Ozgun Babur, Gordon Mills B. Mills, Chris Sander, Anil Korkut. Targeting adaptation to cancer treatment by drug combinations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1759.